Accurately predicting protein–ligand binding affinities and binding modes is a major goal in
computational chemistry, but even the prediction of ligand binding modes in proteins poses …

Ligand binding affinity calculations based on molecular dynamics (MD) simulations and non-
physical (alchemical) thermodynamic cycles have shown great promise for structure-based …

Free energy calculations are used to study how strongly potential drug molecules interact
with their target receptors. The accuracy of these calculations depends on the accuracy of …

The grand challenge in structure-based drug design is achieving accurate prediction of
binding free energies. Molecular dynamics (MD) simulations enable modeling of …

Accurate evaluation of protein–ligand binding free energies in silico is of paramount
importance for understanding the mechanisms of biological regulation and providing a …

Several experimental [1, 2] and computational [3] approaches to fragment-based drug
design have been developed during the past 15 years. The experimental methods are still …

Drug molecules adopt a range of conformations both in solution and in their protein-bound
state. The strain and reduced flexibility of bound drugs can partially counter the …

Cells contain a multitude of different chemical reaction paths running simultaneously and
quite independently next to each other. This amazing feat is enabled by molecular …

Alchemical molecular dynamics simulations for evaluating the binding free energy in ligand-
receptor systems are emerging a new powerful tool for in silico drug discovery projects …

A method is proposed to study protein–ligand binding in a system governed by specific and
nonspecific interactions. Strong associations lead to narrow distributions in the proteins …